[Genome] Table browser / FTP site discrepancy

[Donna Karolchik]

hi Ben,

Looks like you've uncovered a bug in the code that calculates the worst case 
resolution loss number. We've fixed this and it will go out with one of our next 
releases. In the interim, the bug fix is available on our test server at 
http://genome-test.cse.ucsc.edu. Thanks for bringing this to our attention, and 
sorry for any confusion this may have caused.

Needless to say, if you need the data to be accurate, you should use the raw 
data from the file you downloaded, rather than using the compressed data 
available through the Table Browser. I'd like to mention a few things about the 
resolution loss numbers we include in the Table Browser query results. In most 
cases, the number for a value range is calculated for the entire bin(s) of 128 
values, even though the values for only part of the bin(s) may be present in 
your query result. The absolute worst case is displayed -- not all numbers in 
the set will differ that much from the raw values. You should pay particular 
attention to tiny numbers near zero.

-Donna
-----------------------------------
Donna Karolchik
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

----- Original Message ----- 
From: "Benjamin Berman" <benb at fruitfly.org>
To: "UCSC genome browser" <genome at soe.ucsc.edu>
Sent: Monday, November 06, 2006 12:48 PM
Subject: [Genome] Table browser / FTP site discrepancy


>
> I am trying to use the regulatory potential 7 species track for some
> analysis.  I am using hg17.  I first downloaded some regions using
> the table browser.  For chrom 19, position 52426843, I get a value of
> 0.0458949 (see the table browser output .txt file attached to this
> email):
>
> teaview2:~/genome_data/build35_7x_reg_pot.subsets benb$ grep 52426843
> build35_7x_reg_pot_vega_nonbinding.txt
> 52426843        0.0458949
>
> But when i download the entire chromosome wiggle track from the FTP
> server (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/regPotential7X/
> chr19.regPotential7X.hg17.gz), I get a different score of 0.049367:
>
> teaview2:~/genome_data/build35_7x_reg_pot.subsets benb$ grep
> 52426843 ../build35_7x_reg_pot/chr19.regPotential7X.hg17
> 52426843 0.049367
>
> Is this because of the compression alluded to in the table browser
> output?  It says that worst case loss in resolution is 1.7e-05, but
> this is a difference of more than 1e-3.  Do you know why these two
> don't match up more closely?
>
> Thanks for your help,
> Ben Berman
>
>
>


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>
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